SEC23IP

SEC23 interacting protein, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 10:119892706-119944657

Links

ENSG00000107651 ∙ NCBI:11196 ∙ OMIM:617852 ∙ HGNC:17018 ∙ Uniprot:Q9Y6Y8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEC23IP gene.

• Inborn genetic diseases (33 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC23IP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	2	6
missense			33		3	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	33	4	5

Variants in SEC23IP

This is a list of pathogenic ClinVar variants found in the SEC23IP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-119892792-A-G		not specified	Uncertain significance (Nov 18, 2022)
10-119892805-G-C		not specified	Uncertain significance (Dec 13, 2023)
10-119892862-C-T		not specified	Uncertain significance (Jul 09, 2021)
10-119892868-C-T		not specified	Uncertain significance (Aug 22, 2023)
10-119892883-A-G		not specified	Uncertain significance (Dec 22, 2023)
10-119892915-G-A		SEC23IP-related disorder	Benign (Mar 18, 2019)
10-119892930-C-T			Benign (Nov 03, 2018)
10-119898487-C-T		not specified	Uncertain significance (Sep 20, 2023)
10-119898593-A-G			Benign (Dec 20, 2018)
10-119898605-C-T		SEC23IP-related disorder	Likely benign (Dec 26, 2019)
10-119898606-A-G		not specified	Uncertain significance (Aug 28, 2023)
10-119898676-C-T		not specified	Uncertain significance (Feb 10, 2022)
10-119898686-A-T		not specified	Uncertain significance (Jan 04, 2022)
10-119898711-A-G		not specified	Uncertain significance (Aug 01, 2022)
10-119898776-A-T		not specified	Uncertain significance (Sep 01, 2021)
10-119898813-C-T		not specified	Uncertain significance (Jan 10, 2022)
10-119898853-C-T		not specified	Uncertain significance (Sep 01, 2021)
10-119898888-C-T		SEC23IP-related disorder	Benign (Mar 04, 2019)
10-119898942-C-G		not specified	Uncertain significance (Jun 03, 2022)
10-119898955-C-G		not specified	Uncertain significance (Dec 27, 2023)
10-119898958-C-T		not specified	Uncertain significance (Oct 25, 2022)
10-119902841-G-T		not specified	Uncertain significance (Apr 19, 2023)
10-119902901-G-A		not specified	Uncertain significance (Jun 27, 2022)
10-119902910-C-T		SEC23IP-related disorder	Uncertain significance (Jan 10, 2024)
10-119903002-T-A		SEC23IP-related disorder	Uncertain significance (Jan 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC23IP	protein_coding	protein_coding	ENST00000369075	18	49792

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000193	1.00	125651	1	95	125747	0.000382

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.600	503	542	0.927	0.0000276	6542
Missense in Polyphen		162	204.28	0.79302		2361
Synonymous	1.17	174	195	0.893	0.0000102	1932
Loss of Function	4.36	18	51.9	0.347	0.00000274	618

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000918	0.000918
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000467	0.000466
Middle Eastern	0.000218	0.000217
South Asian	0.0000981	0.0000980
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the organization of endoplasmic reticulum exit sites. Specifically binds to phosphatidylinositol 3-phosphate (PI(3)P), phosphatidylinositol 4-phosphate (PI(4)P) and phosphatidylinositol 5-phosphate (PI(5)P). {ECO:0000269|PubMed:10400679, ECO:0000269|PubMed:15623529, ECO:0000269|PubMed:22922100}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

• pRec: 0.226

Intolerance Scores

• loftool: 0.313
• rvis_EVS: 0.16
• rvis_percentile_EVS: 64.96

Haploinsufficiency Scores

• pHI: 0.646
• hipred: N
• hipred_score: 0.414
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.424

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sec23ip
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;COPII vesicle coating
• Cellular component: Golgi membrane;cytoplasm;endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;cytosol;ER to Golgi transport vesicle membrane;COPII-coated ER to Golgi transport vesicle;intracellular membrane-bounded organelle
• Molecular function: RNA binding;phospholipase activity;protein binding;metal ion binding